chrX-152736217-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001166387.4(MAGEA12):āc.56A>Gā(p.Gln19Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,098,153 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001166387.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAGEA12 | NM_001166387.4 | c.56A>G | p.Gln19Arg | missense_variant | 3/3 | ENST00000393869.8 | |
CSAG4 | NR_073432.1 | n.33+2358A>G | intron_variant, non_coding_transcript_variant | ||||
MAGEA12 | NM_001166386.3 | c.56A>G | p.Gln19Arg | missense_variant | 3/3 | ||
MAGEA12 | NM_005367.7 | c.56A>G | p.Gln19Arg | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAGEA12 | ENST00000393869.8 | c.56A>G | p.Gln19Arg | missense_variant | 3/3 | 2 | NM_001166387.4 | P1 | |
MAGEA12 | ENST00000357916.8 | c.56A>G | p.Gln19Arg | missense_variant | 2/2 | 1 | P1 | ||
MAGEA12 | ENST00000393900.4 | c.56A>G | p.Gln19Arg | missense_variant | 3/3 | 1 | P1 | ||
CSAG4 | ENST00000361201.8 | n.33+2358A>G | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183030Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67642
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098153Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363529
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at